Loading python/cpu/3.10.6
  Loading requirement: tk/8.6.8 tcl/8.6.8 qt5/5.11.1
Loading r/4.0.0
  Loading requirement: hdf5/1.10.1 gcc/6.1.0 lapack/gcc/64/3.8.0 jags/4.3.0
    java/1.8 gsl/2.5 pcre2/10.35 libpng/1.6.37 libjpeg/8 udunits/2.2.28
    geos/3.9.1 proj/6.1.0 gdal/3.1.4
SoloTE started at 17:16:38
[OK] samtools found!
[OK] bedtools found!
SoloTE v1.10 started!
SoloTE Home directory /gpfs/data/littmanlab/public/TEpilot/SoloTE
SoloTE executed from /gpfs/data/littmanlab/public/TEpilot/EAEprocessing
Results will be stored in /gpfs/data/littmanlab/public/TEpilot
Input BAM file: /gpfs/data/sequence/results/littmanlab/2019-08-27/cellranger/count-A1/outs/possorted_genome_bam.bam
Input TE BED file: /gpfs/data/littmanlab/public/TEpilot/mm10_rmsk.bed
Currently working in temporary directory: /gpfs/data/littmanlab/public/TEpilot/eae1_SoloTE_temp
samtools view -@ 4 -O BAM -o eae1_nogenes_overlappingtes.bam -L /gpfs/data/littmanlab/public/TEpilot/mm10_rmsk.bed -e '(exists([CB]) && exists([UB]) && [CB]!="-" && [UB]!="-") && (!exists([GN]) || [GN]=="-")' /gpfs/data/sequence/results/littmanlab/2019-08-27/cellranger/count-A1/outs/possorted_genome_bam.bam
samtools index eae1_nogenes_overlappingtes.bam
bedtools bamtobed -i eae1_nogenes_overlappingtes.bam -split > eae1_nogenes_overlappingtes.bed
bedtools intersect -a /gpfs/data/littmanlab/public/TEpilot/mm10_rmsk.bed -b eae1_nogenes_overlappingtes.bed -u > eae1_selectedtes.bed
python /gpfs/data/littmanlab/public/TEpilot/SoloTE/annotateBAM.py eae1_nogenes_overlappingtes.bam eae1_selectedtes.bed temp_annotated_te.bam 1
samtools sort -@ 4 -O BAM -o eae1_teannotated.bam temp_annotated_te.bam
samtools merge --threads 4 -o - /gpfs/data/sequence/results/littmanlab/2019-08-27/cellranger/count-A1/outs/possorted_genome_bam.bam eae1_teannotated.bam|samtools view -@ 4 -O BAM -o eae1_final.bam -e 'exists([CB]) && exists([UB]) && exists([GN]) && [CB]!="-" && [UB]!="-" && [GN]!="-"' --keep-tag GN,CB,UB
samtools index eae1_final.bam
Counts for chromosome 12 are being generated in process: 2149652
Counts for chromosome 13 are being generated in process: 2149652
Counts for chromosome 15 are being generated in process: 2149652
Counts for chromosome 2 are being generated in process: 2149652
Counts for chromosome 6 are being generated in process: 2149652
Counts for chromosome 9 are being generated in process: 2149652
Counts for chromosome JH584304.1 are being generated in process: 2149652
Counts for chromosome 1 are being generated in process: 2149649
Counts for chromosome 14 are being generated in process: 2149649
Counts for chromosome 19 are being generated in process: 2149649
Counts for chromosome 4 are being generated in process: 2149649
Counts for chromosome 8 are being generated in process: 2149649
Counts for chromosome Y are being generated in process: 2149649
Counts for chromosome GL456233.1 are being generated in process: 2149649
Counts for chromosome GL456211.1 are being generated in process: 2149649
Counts for chromosome GL456350.1 are being generated in process: 2149649
Counts for chromosome JH584293.1 are being generated in process: 2149649
Counts for chromosome GL456221.1 are being generated in process: 2149649
Counts for chromosome JH584294.1 are being generated in process: 2149649
Counts for chromosome GL456210.1 are being generated in process: 2149649
Counts for chromosome GL456212.1 are being generated in process: 2149649
Counts for chromosome GL456216.1 are being generated in process: 2149649
Counts for chromosome JH584295.1 are being generated in process: 2149649
Counts for chromosome 10 are being generated in process: 2149650
Counts for chromosome 16 are being generated in process: 2149650
Counts for chromosome 17 are being generated in process: 2149650
Counts for chromosome 5 are being generated in process: 2149650
Counts for chromosome MT are being generated in process: 2149650
Counts for chromosome X are being generated in process: 2149650
Counts for chromosome 11 are being generated in process: 2149651
Counts for chromosome 18 are being generated in process: 2149651
Counts for chromosome 3 are being generated in process: 2149651
Counts for chromosome 7 are being generated in process: 2149651
Traceback (most recent call last):
  File "/gpfs/share/apps/python/cpu/3.10.6/lib/python3.10/site-packages/pandas/core/indexes/range.py", line 345, in get_loc
    return self._range.index(new_key)
ValueError: 4 is not in range

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/gpfs/data/littmanlab/public/TEpilot/SoloTE/SoloTE_pipeline.py", line 226, in <module>
    tecounts2.loc[tecounts2[4].isnull(),4] = tecounts2.loc[tecounts2[4].isnull(),1]
  File "/gpfs/share/apps/python/cpu/3.10.6/lib/python3.10/site-packages/pandas/core/frame.py", line 3761, in __getitem__
    indexer = self.columns.get_loc(key)
  File "/gpfs/share/apps/python/cpu/3.10.6/lib/python3.10/site-packages/pandas/core/indexes/range.py", line 347, in get_loc
    raise KeyError(key) from err
KeyError: 4